] On Behalf Of Ed
Pozharski
Sent: Friday, June 22, 2012 6:14 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] pdb sequence search
Silly question.
Say I want to find every structure in the PDB with the exact sequence or with
perhaps 1-2 mutations. I know of two ways of doing this.
1. Go to NCBI
Hi Ed,
1. Go to NCBI BLAST and run the sequence against the PDB subset. The
resulting list will have identities listed, so manual parsing is doable
if there aren't too many hits.
Have you looked at using NCBI EUtils for this? This might not solve
your problem directly, but it should
Hi Ed,
What about submitting the uniprot accession number of your
protein to the PDB?. As you know, this will just list the all entries
where your protein sequence is there..
-Vandu murugan..
On 6/23/12, Ed Pozharski epozh...@umaryland.edu wrote:
Silly question.
Say I want to find
...@umaryland.edu
Subject: Re: [ccp4bb] pdb sequence search
To: CCP4BB@JISCMAIL.AC.UK
Tim,
I did not understand your objection against solution 1 - is it because
it is not automated? You can sort the results by max. Ident so that
you can sroll down to the limit you set yourself.
More
not get all PDB
files with a DBREF record pointing at the uniprot record of the protein
you want? You can do a simple text search in the PDB, e.g. 'MYG_PHYCA'.
Cheers,Robbie
Date: Fri, 22 Jun 2012 22:39:12 -0400
From: epozh...@umaryland.edu
Subject: Re: [ccp4bb] pdb sequence search
To: CCP4BB
Because I want all the structures of a particular protein itself, not it's
homologues. I just went through several cycles of reducing E-value down to
If you know the UniProt accession code of your protein, then UniPDB is your
friend - pdbe.org/unipdb
If not, try pdbe.org/fasta where you can
Silly question.
Say I want to find every structure in the PDB with the exact sequence or
with perhaps 1-2 mutations. I know of two ways of doing this.
1. Go to NCBI BLAST and run the sequence against the PDB subset. The
resulting list will have identities listed, so manual parsing is
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Hash: SHA1
Dear Ed,
I did not understand your objection against solution 1 - is it because
it is not automated? You can sort the results by max. Ident so that
you can sroll down to the limit you set yourself.
Why do you think a identity cut-off was a good
Tim,
I did not understand your objection against solution 1 - is it because
it is not automated? You can sort the results by max. Ident so that
you can sroll down to the limit you set yourself.
More that it does not generate a list of PDB IDs. What I want to do is
to find every structure
